V. Tanchuk wrote:
Dear Users,
I am trying to simulate Drug – Enzyme Complex accoring to "GROMACS
Tutorial for Drug – Enzyme Complex" with different enzyme (ALKALINE
PHOSPHATASE FROM HUMAN PLACENTA - ZEF1) and ligand. After adding water
with genbox I run:
grompp -f em.mdp -c trp_b4ion.pdb -p trp.top -o trp_b4ion.tpr
This is what I got:
creating statusfile for 1 node...
' for variable integrator, using 'md'
Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'
' for variable ns-type, using 'Grid'
Next time use one of: 'Grid' 'Simple'
' for variable optimize_fft, using 'no'
Next time use one of: 'no' 'yes'
' for variable constraints, using 'none'
Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'
Your .mdp file is badly broken. Windows/Unix file type problem possibly?
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 1284 of the 1485 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
Excluding 3 bonded neighbours for Protein_B 1
Excluding 3 bonded neighbours for DRG 1
Excluding 2 bonded neighbours for SOL 21179
Excluding 2 bonded neighbours for SOL 1711
NOTE:
System has non-zero total charge: -6.999996e+00
processing coordinates...
double-checking input for internal consistency...
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: grompp.c, line: 1109
Fatal error:
There were 4 error(s) processing your input
-------------------------------------------------------
"Working in the Burger Kings, Spitting on your Onion Rings" (Slim Shady)
I would like to know what was wrong with the molecules, but there was
absolutely no indication of that.
Nothing as far as the above says.
Could anyone explain what this 'double-checking' means and how to get
something meaningful of it?
I have also tried some Windows versions (3.2.1, 3.3). They have also
failed, but were able to go beyond this point. Maybe the problem is with
Protein_B which consists of Mg and Zn ions.
I won't rule that out, but it's not the current problem :-)
Mark
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